Atomistry » Copper » PDB 5ce9-5i0y » 5d4j
Atomistry »
  Copper »
    PDB 5ce9-5i0y »
      5d4j »

Copper in PDB 5d4j: Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals

Enzymatic activity of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals

All present enzymatic activity of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals:
1.7.2.1;

Protein crystallography data

The structure of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals, PDB code: 5d4j was solved by Y.Fukuda, K.M.Tse, T.Nakane, T.Nakatsu, M.Suzuki, M.Sugahara, S.Inoue, F.Yumoto, N.Matsugaki, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, M.Yabashi, O.Nureki, M.E.P.Murphy, T.Inoue, S.Iwata, E.Mizohata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.79 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.395, 102.207, 144.506, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23.2

Other elements in 5d4j:

The structure of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals (pdb code 5d4j). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals, PDB code: 5d4j:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5d4j

Go back to Copper Binding Sites List in 5d4j
Copper binding site 1 out of 6 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:30.5
occ:1.00
 ND1 A:HIS145 2.0 23.4 1.0
SG A:CYS136 2.1 28.8 1.0
ND1 A:HIS95 2.3 40.4 1.0
SD A:MET150 2.4 32.7 1.0
CE1 A:HIS145 2.9 25.9 1.0
CG A:HIS145 3.1 25.0 1.0
CB A:CYS136 3.1 26.1 1.0
CE A:MET150 3.2 26.9 1.0
CG A:HIS95 3.3 38.1 1.0
CE1 A:HIS95 3.3 39.2 1.0
CB A:HIS95 3.5 33.9 1.0
CB A:HIS145 3.5 22.2 1.0
CA A:HIS95 3.8 35.0 1.0
CG A:MET150 3.9 32.1 1.0
NE2 A:HIS145 4.0 25.1 1.0
CD2 A:HIS145 4.1 25.4 1.0
CG A:PRO138 4.1 29.0 1.0
O A:MET94 4.3 34.7 1.0
CB A:MET150 4.4 29.1 1.0
CD2 A:HIS95 4.4 40.5 1.0
NE2 A:HIS95 4.4 37.9 1.0
N A:ASN96 4.5 30.7 1.0
SD A:MET62 4.5 34.5 1.0
CA A:CYS136 4.5 28.6 1.0
CD A:PRO138 4.6 27.4 1.0
C A:HIS95 4.7 31.8 1.0
CA A:HIS145 4.8 25.2 1.0
CB A:MET62 4.8 28.9 1.0
N A:HIS95 4.9 35.2 1.0

Copper binding site 2 out of 6 in 5d4j

Go back to Copper Binding Sites List in 5d4j
Copper binding site 2 out of 6 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:31.0
occ:1.00
 NE2 A:HIS135 2.1 26.0 1.0
NE2 A:HIS100 2.1 23.5 1.0
NE2 C:HIS306 2.1 26.4 1.0
CL C:CL601 2.3 53.2 1.0
CD2 A:HIS135 2.9 27.0 1.0
CE1 A:HIS100 2.9 24.6 1.0
CE1 C:HIS306 3.0 26.7 1.0
CD2 C:HIS306 3.2 25.7 1.0
CE1 A:HIS135 3.2 26.5 1.0
CD2 A:HIS100 3.2 25.8 1.0
OD2 A:ASP98 3.9 44.2 1.0
NE2 C:HIS255 4.1 31.7 1.0
CG A:HIS135 4.1 25.8 1.0
ND1 A:HIS100 4.1 25.4 1.0
ND1 C:HIS306 4.2 26.6 1.0
ND1 A:HIS135 4.2 28.4 1.0
CG A:HIS100 4.3 27.5 1.0
CG C:HIS306 4.3 26.4 1.0
CE1 C:HIS255 4.3 34.5 1.0
CG A:ASP98 4.3 35.3 1.0
CD2 C:HIS255 4.4 35.8 1.0
OD1 A:ASP98 4.6 29.6 1.0
ND1 C:HIS255 4.7 31.4 1.0
CD2 C:LEU308 4.8 23.5 1.0
CG C:HIS255 4.8 34.3 1.0

Copper binding site 3 out of 6 in 5d4j

Go back to Copper Binding Sites List in 5d4j
Copper binding site 3 out of 6 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:32.1
occ:1.00
 ND1 B:HIS145 2.1 28.8 1.0
SG B:CYS136 2.1 31.7 1.0
ND1 B:HIS95 2.2 28.7 1.0
SD B:MET150 2.4 31.5 1.0
CE1 B:HIS145 2.9 30.5 1.0
CG B:HIS145 3.1 29.3 1.0
CG B:HIS95 3.2 29.8 1.0
CE1 B:HIS95 3.2 28.3 1.0
CB B:CYS136 3.2 31.2 1.0
CE B:MET150 3.2 27.1 1.0
CB B:HIS95 3.4 29.8 1.0
CB B:HIS145 3.6 26.9 1.0
CA B:HIS95 3.8 29.7 1.0
CG B:MET150 3.8 28.1 1.0
NE2 B:HIS145 4.0 27.2 1.0
CD2 B:HIS145 4.1 28.2 1.0
CG B:PRO138 4.2 31.4 1.0
O B:MET94 4.2 34.4 1.0
NE2 B:HIS95 4.3 29.0 1.0
CD2 B:HIS95 4.3 28.3 1.0
CB B:MET150 4.4 26.2 1.0
SD B:MET62 4.4 30.8 1.0
CD B:PRO138 4.5 27.8 1.0
CA B:CYS136 4.6 29.4 1.0
N B:ASN96 4.7 32.2 1.0
N B:HIS95 4.7 31.5 1.0
C B:HIS95 4.8 36.2 1.0
CA B:HIS145 4.8 27.0 1.0
CB B:MET62 4.9 31.0 1.0
C B:MET94 4.9 32.4 1.0

Copper binding site 4 out of 6 in 5d4j

Go back to Copper Binding Sites List in 5d4j
Copper binding site 4 out of 6 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:30.2
occ:1.00
 NE2 B:HIS100 2.0 22.3 1.0
NE2 A:HIS306 2.1 30.9 1.0
NE2 B:HIS135 2.1 30.1 1.0
CL A:CL503 2.3 63.3 1.0
CE1 B:HIS100 2.9 23.0 1.0
CE1 A:HIS306 2.9 30.6 1.0
CD2 B:HIS135 2.9 27.2 1.0
CD2 B:HIS100 3.1 24.7 1.0
CD2 A:HIS306 3.2 30.8 1.0
CE1 B:HIS135 3.2 28.9 1.0
OD2 B:ASP98 3.8 41.4 1.0
ND1 B:HIS100 4.0 21.4 1.0
ND1 A:HIS306 4.1 31.2 1.0
CG B:HIS135 4.1 28.3 1.0
NE2 A:HIS255 4.2 29.9 1.0
CG B:HIS100 4.2 23.9 1.0
ND1 B:HIS135 4.3 26.0 1.0
CG A:HIS306 4.3 29.9 1.0
CG B:ASP98 4.4 35.2 1.0
CE1 A:HIS255 4.4 30.9 1.0
CD2 A:HIS255 4.5 30.0 1.0
OD1 B:ASP98 4.7 33.9 1.0
O A:HOH664 4.8 29.6 1.0
CD2 A:LEU308 4.8 24.9 1.0
ND1 A:HIS255 4.9 29.9 1.0
CG A:HIS255 5.0 31.6 1.0

Copper binding site 5 out of 6 in 5d4j

Go back to Copper Binding Sites List in 5d4j
Copper binding site 5 out of 6 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu602

b:29.2
occ:1.00
 ND1 C:HIS145 2.1 27.8 1.0
ND1 C:HIS95 2.1 26.8 1.0
SG C:CYS136 2.3 24.9 1.0
SD C:MET150 2.5 30.1 1.0
CE1 C:HIS145 2.9 26.4 1.0
CG C:HIS95 3.0 25.4 1.0
CE1 C:HIS95 3.1 26.2 1.0
CG C:HIS145 3.2 28.1 1.0
CB C:CYS136 3.2 26.3 1.0
CB C:HIS95 3.3 24.3 1.0
CE C:MET150 3.3 27.1 1.0
CB C:HIS145 3.6 25.7 1.0
CA C:HIS95 3.8 27.1 1.0
CG C:MET150 3.9 24.1 1.0
NE2 C:HIS145 4.1 27.3 1.0
CD2 C:HIS95 4.2 25.6 1.0
O C:MET94 4.2 29.8 1.0
CD2 C:HIS145 4.2 26.8 1.0
NE2 C:HIS95 4.2 27.9 1.0
CG C:PRO138 4.4 24.5 1.0
CB C:MET150 4.4 25.2 1.0
SD C:MET62 4.4 33.2 1.0
CD C:PRO138 4.6 24.4 1.0
N C:ASN96 4.7 26.4 1.0
CA C:CYS136 4.7 28.3 1.0
CA C:HIS145 4.8 27.2 1.0
N C:HIS95 4.8 28.9 1.0
C C:HIS95 4.8 25.5 1.0
CB C:MET62 4.9 28.5 1.0
C C:MET94 4.9 30.6 1.0

Copper binding site 6 out of 6 in 5d4j

Go back to Copper Binding Sites List in 5d4j
Copper binding site 6 out of 6 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu603

b:27.8
occ:1.00
 NE2 C:HIS100 2.0 28.5 1.0
NE2 B:HIS306 2.1 24.5 1.0
NE2 C:HIS135 2.1 24.4 1.0
CL B:CL503 2.2 49.2 1.0
CE1 C:HIS100 2.9 25.7 1.0
CE1 B:HIS306 3.0 24.6 1.0
CD2 C:HIS135 3.0 24.7 1.0
CD2 B:HIS306 3.1 28.0 1.0
CE1 C:HIS135 3.1 27.1 1.0
CD2 C:HIS100 3.2 27.3 1.0
OD2 C:ASP98 3.7 32.1 1.0
ND1 C:HIS100 4.0 24.8 1.0
ND1 B:HIS306 4.1 24.1 1.0
NE2 B:HIS255 4.2 28.4 1.0
CG C:HIS135 4.2 26.4 1.0
ND1 C:HIS135 4.2 26.8 1.0
CG B:HIS306 4.2 23.4 1.0
CG C:HIS100 4.2 26.1 1.0
CG C:ASP98 4.4 30.1 1.0
CE1 B:HIS255 4.4 27.4 1.0
CD2 B:HIS255 4.5 28.7 1.0
OD1 C:ASP98 4.7 29.2 1.0
ND1 B:HIS255 4.8 28.4 1.0
CD2 B:LEU308 4.8 22.5 1.0
O C:HOH808 4.9 27.9 1.0
CG B:HIS255 4.9 29.6 1.0
CD1 B:LEU308 5.0 21.1 1.0

Reference:

Y.Fukuda, K.M.Tse, T.Nakane, T.Nakatsu, M.Suzuki, M.Sugahara, S.Inoue, T.Masuda, F.Yumoto, N.Matsugaki, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, T.Hatsui, M.Yabashi, O.Nureki, M.E.Murphy, T.Inoue, S.Iwata, E.Mizohata. Redox-Coupled Proton Transfer Mechanism in Nitrite Reductase Revealed By Femtosecond Crystallography Proc.Natl.Acad.Sci.Usa V. 113 2928 2016.
ISSN: ESSN 1091-6490
PubMed: 26929369
DOI: 10.1073/PNAS.1517770113
Page generated: Wed Jul 31 04:00:53 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy